R Notebook

Covid API provided by UK government

library(ukcovid19)
query_filters <- c(
  'areaType=nation',
  'areaName=England'
)
cases_and_deaths = list(
  date = "date",
  cumCasesBySpecimenDateRate = "cumCasesBySpecimenDateRate",
  cumDeaths28DaysByDeathDate = "cumDeaths28DaysByDeathDate"
)

df <- get_data(
  filters = query_filters, 
  structure = cases_and_deaths
)

library(ggplot2)
library(tidyverse)
library("drc")
library(plotly)

# set functions to convert to days 
toDays <- function(x){
 day <-  ceiling((as.numeric(x) - min(as.numeric(x)))/86400)
 return(day)
}

df$date <- as.POSIXct(df$date)
df = na.omit(df)

Overview - Up-todate Covid Situation

startDate = "2021-03-01"
endDate = "2021-7-27"

filter <- (df$date >= startDate)&(df$date <= endDate)
x <- df[filter,] %>%
  ggplot(aes(x = date, y = cumDeaths28DaysByDeathDate)) + 
  geom_line(color = "blue") + 
  ylab("cumulative death") + 
  theme(panel.border = element_blank(),
          panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_rect(fill = "#fafafa"),
          plot.background = element_rect(fill = "white")
        )
ggplotly(x, tooltip = c("date"))

Select Time Periord For Analysis

startDate = "2021-02-23"
endDate = "2021-7-26"

cutPoint = "2021-05-23"
filter1 <- (df$date >= startDate)&(df$date <= endDate)
block1 <- df[filter1,]
block1$day = toDays(block1$date)

ts <- subset(block1, date < cutPoint , c(date, day, cumDeaths28DaysByDeathDate))
vs <- subset(block1, date >= cutPoint, c(date, day, cumDeaths28DaysByDeathDate))
ts

#Weibull <- drm(cumDeaths28DaysByDeathDate ~ day, fct = W1.3(), data = ts)

Viz

#calcuate xlim
ts$cumDeaths28DaysByDeathDate %>%
  min() -> ymin
vs$cumDeaths28DaysByDeathDate %>%
  max() -> ymax
vs$day %>%
  max() -> xmax
with(ts, plot(x = day, y = cumDeaths28DaysByDeathDate, 
              xlim = c(0, xmax), main = "Validation",
            ylim = c(ymin,ymax), col = "grey51", type = "h",
            xlab = "Days since day 0",
            ylab = "Cumulative Death")
  )
with(vs, points(x = day, y = cumDeaths28DaysByDeathDate, col = "grey87", type = "h"))